Applying XClone to mouse scRNA-seq: xcltk pre-processing for BAF data

[NickolasTeo]

To prepare scRNA-seq data for BAF analysis, xcltk is used. However, xcltk current does not support mm10 mouse scRNA-seq data at the baf_pre_phase.sh step, as it only permits usage of a Sanger-phasing hg19 fasta file, and not mm10

Additionally, heterozygous SNPs is identified via the Sanger Imputation Server. Are there alternatives to make this process applicable to mouse scRNA as well?

Lastly, baf_post_phase.sh only supports hg19 or hg38, and not mm10

[Rongtingting]

@hxj5

[hxj5]

Hi, I initialize the scripts and data for preprocessing BAF signal on mouse scRNA-seq data (see xcltk/preprocess_mouse folder under the mouse branch). For now, you may clone the repo to local machine and switch to "mouse" branch, then try running the script baf_pre_phase.mouse.sh to call heterozygous SNPs (commit 303d4bc). Please modify the example pre-phase cmdline to make it work on mouse data. The phasing and post-phasing parts would be updated if sufficient heterozygous SNPs were detected.